Alignments for a candidate for malK_Ss in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for malK_Ss in Pseudomonas fluorescens FW300-N2E3

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate AO353_05410 AO353_05410 peptide ABC transporter ATP-binding protein

Query= TCDB::Q97UG5
         (617 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05410
          Length = 323

 Score =  189 bits (481), Expect = 1e-52
 Identities = 104/267 (38%), Positives = 170/267 (63%), Gaps = 9/267 (3%)

Query: 355 VVMKILNLSKIYYIRKNLILSEP-INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAG 413
           VV+   +L++ Y + + L      + A+N VSFEL+ G   A+VG SG GKST+A+ L  
Sbjct: 3   VVLTARDLTRHYEVSRGLFKGTALVRALNGVSFELEAGKTLAVVGESGCGKSTLARALTL 62

Query: 414 MIQQTSGKIILLGKDVSEYGVRNSMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHK 473
           + + +SG + + G++V+          +++VQM+FQ PY+SL+PR  +   +  PLLI+ 
Sbjct: 63  IEEPSSGSLKIAGQEVTGANKAERKQLRKDVQMVFQSPYASLNPRQKIGDQLAEPLLINT 122

Query: 474 KVSNKDQLLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADE 533
           K+S  ++   K+  ++K VGL+P  ++  +YPH  SGG+RQR+A+ARA  ++PKVLVADE
Sbjct: 123 KLSAAER-REKVQAMMKQVGLRP--EHYQRYPHMFSGGQRQRIALARAMMLQPKVLVADE 179

Query: 534 PVSMLDASLRAGILNLIKKFKKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTY 592
           P S LD S++A +LNL    ++    + ++I+H++A V ++AD+++V+Y GR VE G   
Sbjct: 180 PTSALDVSIQAQVLNLFMDLQQEFNTAYVFISHNLAVVRHVADQVLVMYLGRPVEMGPKE 239

Query: 593 EVISNPSHEYTKRLIEAV----PDPYK 615
           ++ + P H YT+ L+ A     PDP K
Sbjct: 240 DIYTRPLHPYTQALLSATPTIHPDPTK 266



 Score =  178 bits (452), Expect = 3e-49
 Identities = 105/308 (34%), Positives = 174/308 (56%), Gaps = 9/308 (2%)

Query: 13  ELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVVLRGH 72
           E++ G F     V  +  V+FE+   +  A+ GESGCGKSTLA A+  L++ P     G 
Sbjct: 15  EVSRGLFKGTALVRALNGVSFELEAGKTLAVVGESGCGKSTLARALT-LIEEPS---SGS 70

Query: 73  VYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAA-VSHGVNVEEA 131
           + +  +++    + E ++LR K+   V Q    +L+P  KIGDQ+     ++  ++  E 
Sbjct: 71  LKIAGQEVTGANKAERKQLR-KDVQMVFQSPYASLNPRQKIGDQLAEPLLINTKLSAAER 129

Query: 132 RKLIKEKLELVDLPYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTTGLDVIVQ 191
           R+ ++  ++ V L       YPH  SGG RQR+ +A +++L P +++ DEPT+ LDV +Q
Sbjct: 130 REKVQAMMKQVGLRPEHYQRYPHMFSGGQRQRIALARAMMLQPKVLVADEPTSALDVSIQ 189

Query: 192 YEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIKRPSHPY 251
            ++L     +Q++   + V ISH+++++  ++D+V +MY G  VE+G KE+I  RP HPY
Sbjct: 190 AQVLNLFMDLQQEFNTAYVFISHNLAVVRHVADQVLVMYLGRPVEMGPKEDIYTRPLHPY 249

Query: 252 TYLLISSLPSLVKRREK-LLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLNPALGDI 310
           T  L+S+ P++     K  + I G  P  L+  P+ C F+ RCP+  E CS   PAL   
Sbjct: 250 TQALLSATPTIHPDPTKPKIKIVGELPNPLNP-PSGCAFHKRCPYATELCSKEEPALRQ- 307

Query: 311 MDGHKARC 318
           +D  +  C
Sbjct: 308 LDSRQVAC 315


Lambda     K      H
   0.319    0.138    0.391 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 497
Number of extensions: 24
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 617
Length of database: 323
Length adjustment: 32
Effective length of query: 585
Effective length of database: 291
Effective search space:   170235
Effective search space used:   170235
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources